Hello, I'm a big fan of Evernote and the web clipper and usually prefer using it on Mac OS with Safari. So when I found out about this issue I researched it and thought I would share my findings after contacting Evernote support. They replied very quickly, even on a Sunday night 🙂.
Apple is no longer supporting 'legacy' Extensions on Safari 12.x. This issue is caused by the macOS Catalina 64-bit architecture change. In Mojave, the app architecture takes a hybrid approach, allowing 32-bit and 64-bit, but providing a warning if you are using 32-bit apps. If you are running Catalina like I am, 32-bit apps will not be supported, period. Therefore if you want web clipper functionality on MacOS Catalina, there are two options, according to Evernote support. Neither of them mean that as I write this (Monday September 9, 2019) that you can use Safari immediately with the Evernote web clipper. Third option is don't upgrade right now to Catalina.
1. Switch to Chrome for Mac OS, [which is what I am doing at least temporarily] and use it with Evernote web clipper. Apple has unilaterally removed what it considers to now be 'legacy' 32-bit applications from the App Store. That's why you can't find Evernote web clipper there any more.
2. Wait for few weeks or months for the Evernote architecture and Mac OS Catalina 64-bit architecture / Safari 12.x architecture to get back in synch.
3. If you are running Mojave, you could also delay upgrading to Mac OS Catalina. However, there are other benefits to staying current with operating system updates. Additionally, 64-bit architecture on Apple OS promises to be faster.
I'm including a screen shot from the web site MacPaw with a good explanation of the 32-bit vs. 64-bit issue. It explains what the issue is, how Catalina sends warnings of the 32-bit issue, and how to find all 32-bit applications running on your Mac.
For me, this non-64-bit list (i.e. legacy 32-bit list) also included:
1. Adobe application manager
2. Quickbooks

Thank you for your reply jefito. You clarified the situation but I would like Evernote to handle this situation more gracefully.
1. I merged several notes into a single note; each note had a scanned PDF which was created with the Evernote Edition ScanSnap scanner (love it).
2. I am running the Evernote Mac desktop client, though I also run Evernote Android and iOS Apps on two mobile phones.
I did not move notes to a different notebook.
I do see the notes in the trash now, which is helpful to know now, but, having entered the problem this morning and not being able to intuitively find the notes I spend about 2 hours redoing the work today and just checked back on this support thread in the evening. Moving original notes to the trash, when no merged note appears is not the behavior I would hope for, but thanks for clarifying.

This bug still exists as of 11/8/17. I just spent quite a bit of time creating notes with PDF scanned documents. I wanted to merge notes together. The first thing I saw was that if I merged ALL notes, they exceeded a 200 MB limit. So, I merged a subset of the notes which fell below 200MB. Poof. All the notes I merged were gone and there was no merged note.